Crop domestication allowed humans to select for desirable agronomic characteristics and marked a major turning point in the human and earth history. However, this artificial selection, which was accelerated over the past decades by intense breeding activities, resulted in most modern cultivars and hybrids to exhibit low genetic diversity compared to the respective wild relatives. Consequently, elite varieties and hybrids widely used in agriculture, lack important resistances to devastating pathogens and pests, and often hold limited tolerance to abiotic constrains. Fostered by a global demand for an eco-friendly agriculture, crop breeders put effort to identify disease-resistance genes in the wild crop ancestors and breed them into elite germplasms. In practice, the type of resistance commonly employed in breeding programs is the so-called qualitative resistance which is based on single R-genes that follow simple mendelian inheritance. Although R-gene mediated resistance provides complete or near complete protection, is often not durable and imposes a fitness penalty on the crop. However, there is an ex planta genome on which plants largely depend for optimal performance, and this genome remains largely unexplored in crop breeding for its potential to provide durable protection against pathogens with no apparent fitness cost for the host. This expanded genome, the so-called plant microbiome, is built up by the communities of microbes which live in close association with the plants and collectively referred to as the plant microbiota.

 

MICROBREED focuses on tomato and follows a multidisciplinary approach to reach the following objectives:

 

 i.     Develop a HTS platform for microbiota-informed plant breeding and utilize this platform to identify tomato accessions (crop genitors) which support in their rhizosphere potent growth-promoting and disease-suppressive microbial communities.

 

ii.   Profile the prominent communities of growth-promoting and disease-suppressive rhizobacteria by employing 16s rRNA gene sequencing and utilize the metagenomic data to isolate individual strains for the purpose of designing functional synthetic communities of reduced complexity.

 

iii.  Analyze the functional diversity of the growth-promoting and disease-suppressive natural and synthetic microbial communities by shotgun metagenomics and whole-genome sequencing of the individual community members.

 

iv.    Unravel the mechanism involved in microbiota-mediated plant disease resistance by employing forward genetics screens in synthetic community members and further profile local (roots) and systemic (leaves) whole-genome transcriptional changes in response to root bacterization by synthetic microbial communities.